def test_mopac_3(configuration):
check_symbols = [
"Cu",
"Cu",
"Cu",
"Cu",
"Br",
"Br",
"Br",
"Br",
"Br",
"Br",
"Br",
"Br",
"Br",
"Br",
]
check_smiles = "Br[Cu]([Cu][Cu](Br)(Br)(Br)Br)(Br)Br.Br[Cu](Br)Br"
file_name = build_filenames.build_data_filename("Cu(II)4Br10(2-) (CIVNAW10).mop")
read_structure_step.read(file_name, configuration)
if configuration.atoms.symbols != check_symbols:
print(configuration.atoms.symbols)
smiles = configuration.canonical_smiles
if smiles != check_smiles:
print(smiles)
assert configuration.atoms.symbols == check_symbols
assert smiles == check_smiles
def test_mopac_6(configuration):
check_symbols = ["F", "K", "F", "K"]
check_smiles = "F[K].F[K]"
file_name = build_filenames.build_data_filename("potassium fluoride, dimer.mop")
read_structure_step.read(file_name, configuration)
if configuration.atoms.symbols != check_symbols:
print(configuration.atoms.symbols)
smiles = configuration.canonical_smiles
if smiles != check_smiles:
print(smiles)
assert configuration.atoms.symbols == check_symbols
assert smiles == check_smiles
def test_mopac_2(configuration):
check_symbols = ["Li", "F", "Li", "F", "Li", "F"]
check_smiles = "[Li]F.[Li]F.[Li]F"
file_name = build_filenames.build_data_filename("lithium fluoride, trimer.mop")
read_structure_step.read(file_name, configuration)
if configuration.atoms.symbols != check_symbols:
print(configuration.atoms.symbols)
smiles = configuration.canonical_smiles
if smiles != check_smiles:
print(smiles)
assert configuration.atoms.symbols == check_symbols
assert smiles == check_smiles
def test_extensions(configuration, file_name, extension):
xyz_file = build_filenames.build_data_filename(file_name)
read_structure_step.read(xyz_file, configuration, extension=extension)
assert configuration.n_atoms == 3
assert all(atom in ["O", "H", "H"] for atom in configuration.atoms.symbols)
coordinates = configuration.atoms.coordinates
assert len(coordinates) == 3
assert all(len(point) == 3 for point in coordinates)
assert configuration.bonds.n_bonds == 2
if str(configuration.bonds) != bond_string:
print(configuration.bonds)
assert str(configuration.bonds) == bond_string
def test_mopac(configuration):
file_name = build_filenames.build_data_filename("acetonitrile.mop")
read_structure_step.read(file_name, configuration)
assert configuration.n_atoms == 6
assert all(
atom in ["H", "H", "H", "C", "C", "N"] for atom in configuration.atoms.symbols
)
coordinates = configuration.atoms.coordinates
assert len(coordinates) == 6
assert all(len(point) == 3 for point in coordinates)
assert configuration.bonds.n_bonds == 5
if str(configuration.bonds) != acetonitrile_bonds:
print(configuration.bonds)
assert str(configuration.bonds) == acetonitrile_bonds
def test_mopac_8(configuration):
check_symbols = [
"C",
"H",
]
check_smiles = "[CH]"
file_name = build_filenames.build_data_filename("methylidyne.mop")
read_structure_step.read(file_name, configuration)
if configuration.atoms.symbols != check_symbols:
print(configuration.atoms.symbols)
smiles = configuration.canonical_smiles
if smiles != check_smiles:
print(smiles)
assert configuration.atoms.symbols == check_symbols
assert smiles == check_smiles
def test_format(configuration, structure):
file_name = build_filenames.build_data_filename(structure)
read_structure_step.read(file_name, configuration)
assert configuration.n_atoms == 10
assert all(
atom in ["N", "N", "N", "N", "C", "C", "H", "H", "H", "H"]
for atom in configuration.atoms.symbols
)
coordinates = configuration.atoms.coordinates
assert len(coordinates) == 10
assert all(len(point) == 3 for point in coordinates)
assert configuration.bonds.n_bonds == 10
if "xyz" in structure:
if str(configuration.bonds) != xyz_bond_string:
print(configuration.bonds)
assert str(configuration.bonds) == xyz_bond_string
else:
if str(configuration.bonds) != bond_string:
print(configuration.bonds)
assert str(configuration.bonds) == bond_string
def test_sanitize_file_format_regex_validation(configuration):
with pytest.raises(NameError):
read_structure_step.read("spc.xyz", configuration, extension=".xy-z")
def test_mopac_7(configuration):
check_symbols = [
"Cr",
"O",
"O",
"O",
"O",
"O",
"O",
"C",
"C",
"C",
"C",
"C",
"C",
"Cr",
"C",
"C",
"O",
"O",
"O",
"O",
"O",
"C",
"C",
"C",
"O",
"C",
"H",
"H",
"H",
"H",
"H",
"H",
"H",
"H",
"H",
"H",
"H",
"H",
"H",
"H",
"H",
"H",
"H",
"H",
"H",
"H",
]
check_smiles = "C[C](O[Cr]12(OC(=O)C)O[C](O[Cr]2(O[C](O)C)(OC(=O)C)O[C](O1)C)C)O"
file_name = build_filenames.build_data_filename("Cr_ACETCR.mop")
read_structure_step.read(file_name, configuration)
if configuration.atoms.symbols != check_symbols:
print(configuration.atoms.symbols)
smiles = configuration.canonical_smiles
if smiles != check_smiles:
print(smiles)
assert configuration.atoms.symbols == check_symbols
assert smiles == check_smiles
def test_mopac_4(configuration):
check_symbols = [
"Eu",
"N",
"N",
"N",
"N",
"N",
"N",
"O",
"O",
"O",
"O",
"C",
"C",
"C",
"C",
"C",
"C",
"C",
"C",
"C",
"C",
"C",
"C",
"C",
"C",
"C",
"C",
"C",
"C",
"C",
"C",
"C",
"C",
"C",
"C",
"C",
"C",
"H",
"H",
"H",
"H",
"H",
"H",
"H",
"H",
"H",
"H",
"H",
"H",
"H",
"H",
"H",
"H",
"H",
"H",
"H",
"H",
"H",
"H",
"H",
"H",
"H",
"H",
"H",
"H",
"H",
"H",
"H",
"H",
]
check_smiles = (
r"C[C]1c2cccc(n2)/C(=N/CC[N@]2[Eu]34([N@@]1CC/N=C(\C)/c1nc([C]2C)ccc1)"
r"(O[C](O3)C)O[C](O4)C)/C"
)
file_name = build_filenames.build_data_filename(
"RM1 63 Europium, CCDC entry LAPJAN.mop"
)
read_structure_step.read(file_name, configuration)
if configuration.atoms.symbols != check_symbols:
print(configuration.atoms.symbols)
smiles = configuration.canonical_smiles
if smiles != check_smiles:
print(smiles)
assert configuration.atoms.symbols == check_symbols
assert smiles == check_smiles
def test_unregistered_reader(configuration):
with pytest.raises(KeyError):
xyz_file = build_filenames.build_data_filename("spc.xyz")
read_structure_step.read(xyz_file, configuration, extension=".mp3")
def test_empty_filename(configuration):
with pytest.raises(NameError):
read_structure_step.read("", configuration)
def test_read_filename_type(configuration, file_name):
with pytest.raises(TypeError):
read_structure_step.read(file_name, configuration)
